Back in 1790, the legal system was much more patriarchal than it is now--married women were more or less like children in the eyes of the law. So the father's status carried more weight than the mother's. The law changing that in the 1920s came after the amendment that gave women the right to vote, when social and legal attitudes had changed.
Sen. McCain was on one of the morning shows yesterday and falsely asserted that he himself had been born in the Panama Canal Zone, rather than in Panama proper.
Your reasoning might better be applied to the question regarding how it is considered that persons in the service of the USA who have children born outside of CONUS could have their (the children’s) natural heritage be revoked. That is just plain stupid and unlikely something which would ever have been supported by any Founder.